rs878853029
Positions:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4BP6_Moderate
The NM_004426.3(PHC1):c.1598G>A(p.Arg533Gln) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000078 ( 0 hom., cov: 19)
Exomes 𝑓: 0.000018 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PHC1
NM_004426.3 missense
NM_004426.3 missense
Scores
2
8
8
Clinical Significance
Conservation
PhyloP100: 8.37
Genes affected
PHC1 (HGNC:3182): (polyhomeotic homolog 1) This gene is a homolog of the Drosophila polyhomeotic gene, which is a member of the Polycomb group of genes. The gene product is a component of a multimeric protein complex that contains EDR2 and the vertebrate Polycomb protein BMH1. The gene product, the EDR2 protein, and the Drosophila polyhomeotic protein share 2 highly conserved domains, named homology domains I and II. These domains are involved in protein-protein interactions and may mediate heterodimerization of the protein encoded by this gene and the EDR2 protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.2760085).
BP6
?
Variant 12-8933055-G-A is Benign according to our data. Variant chr12-8933055-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 235403.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHC1 | NM_004426.3 | c.1598G>A | p.Arg533Gln | missense_variant | 8/15 | ENST00000544916.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHC1 | ENST00000544916.6 | c.1598G>A | p.Arg533Gln | missense_variant | 8/15 | 1 | NM_004426.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000775 AC: 1AN: 128988Hom.: 0 Cov.: 19
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000178 AC: 10AN: 560286Hom.: 0 Cov.: 7 AF XY: 0.0000206 AC XY: 6AN XY: 290620
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GnomAD4 genome ? AF: 0.00000775 AC: 1AN: 128988Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0AN XY: 60846
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 18, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;T;D
Polyphen
D;.;D
Vest4
MutPred
Loss of solvent accessibility (P = 1e-04);.;Loss of solvent accessibility (P = 1e-04);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at